Semiempirical study of compounds with intramolecular O?H…︁O hydrogen bonds. II. Further verification of a modified MNDO method

In the forerunner of this article, we described a MNDO modification designed for studies of compounds with intramolecular O? H…?O hydrogen bonds. Here, we report the further verification of the modification by means of its application to 14 compounds not considered in its development. Comparison of the calculated structural parameters and proton transfer characteristics with available experimental or ab initio results, and with those obtained using MNDO, AM1, MNDO/H, MNDO/M, and PM3, supports the validity of the new modification for prediction of hydrogen bond characteristics. © 1994 by John Wiley & Sons, Inc.     

Anomalous Enhancement of Proton Conductivity for Water Molecular Clusters Stabilized in Interstitial Spaces of Porous Molecular Crystals

In an investigation into the proton conductivity of crystallized water clusters confined within low‐dimensional nanoporous materials, we have found that water‐stable nanoporous crystals are formed by complementary hydrogen bonding between [Co^III(H₂bim)₃]³⁺ (H₂bim: 2,2′‐biimidazole) and TATC^3? (1,3,5‐ tricarboxyl‐2,4,6‐triazinate); the O atoms in the ?COO^? groups of TATC^3? in the porous outer wall are strongly hydrogen bonded with H₂O, forming two types of WMCs (water molecular clusters): a spirocyclic tetramer chain (SCTC) that forms infinite open 1D channels, and an isolated cyclic tetramer (ICT) present in the void space. The ICT is constructed from four H₂O molecules as a novel C₂‐type WMC, which are hydrogen bonded with four‐, three‐, and two‐coordination spheres, respectively. The largest structural fluctuation is observed at elevated temperatures from the two‐coordinated H₂O molecules, which begin to rapidly and isotropically fluctuate on heating. This behavior can be rationalized by a simple model for the elucidation of pre‐melting phenomena, similar to those in ice surfaces as the temperature increases. Moreover, high proton conductivity of SCTCs (ca. 10^?5 S cm^?1 at 300 K with an activation energy of 0.30 eV) through a proton‐hole mechanism was observed for pellet samples using the alternating impedance method. The proton conductivity exhibits a slight enhancement of about 0.1×10^?5 S cm^?1 at 274 K due to a structural transition upon approaching this temperature that elongates the unit cell along the b‐axis. The proton‐transfer route can be predicted in WMCs, as O(4) of an H₂O molecule at the center of an SCTC shows a motion that rotates the dipole in the b‐axis direction, but not the c‐axis; the thermal ellipsoids of O(4) based on anisotropic temperature factors obtained by X‐ray crystallography reflect a structural fluctuation along the b‐axis direction induced by [Co^III(H₂bim)₃]³⁺.     

A DFT study of the hydrolysis of hydantoin

Density functional theory (DFT) calculations were made on the hydrolysis of hydantoin (2,4-imidazolidinedione). In the neutral hydrolysis, reacting systems composed of hydantoin and (H₂O)_n with n = 1+3, 2+3, 3+3, and 4+3 were adopted. Three water molecules (“+3”) participate in the in-plane hydrogen-bond circuit, and the n–3 = 1, 2, 3 or 4 water cluster works for the out-of-plane nucleophilic attack onto the carbonyl carbon of hydantoin. Transition states (TSs) involving bond interchanges prompted by proton transfers were determined. The reaction path with n = 3+3 containing N-carbamoyl glycine, N-carboxy glycine and three tetrahedral intermediates was found to be most likely. In the acid-catalyzed hydrolysis, a reacting system composed of hydantoin and H₃O⁺(H₂O)₇ was employed. Ten TSs and nine intermediates were obtained. N-carbamoyl glycine and N-carboxy glycine were confirmed to be detectable stable species. The product consists of glycine, carbonic acid (not CO₂), NH₄⁺, and (H₂O)₅. It has the exothermic energy, whereas the product in the neutral hydrolysis is of the endothermic one for all n values. For both neutral (n = 3+3) and acid-catalyzed hydrolyses, the rate-determining steps were calculated to be for formation of the tetrahedral intermediate, HOOC-CH₂-NH-C(OH)₂NH₂. The pattern of proton transfers along hydrogen bonds was carefully investigated.     

Molecular orbital study of the effects of ionic amino acid residues on proton transfer energetics in the active site of carboxypeptidase a

As part of a study of the catalytic mechanism of carboxypeptidase A, two proton transfers in the system Glu 270 H₂OZnHis 69-Asp 142 are treated with an ab initio MO method. Results show that the proton transfers are strongly affected by the environment. It is predicted that the proton between His 69 and Asp 142 is covalently bonded to His 69.     

An analysis of predictions by the semi-empirical MNDO molecular orbital method for some aspects of molecular energetics

Calculations using the MNDO HE molecular-orbital method predict that NH₄, PH₄ and H₃S are stable free radicals, and that local minima exist for H₃O and H₂Cl. The tendency of MNDO to overestimate the stability of such systems is traced to its neglect of overlap integrals. Results for H⁺₂ (both ground and excited states) support this conclusion. Stable radicals with formulas BeH₃ and BH₄ are also predicted. Analysis of hydrocarbon thermochemistry indicates that MNDO fails to predict the correct sign for the relative magnitude of bond interactions, whereas ab initio calculations give the correct sign and approximately the correct magnitude. Finally, it is shown that the apparent superiority of MNDO over ab initio MO calculations in predicting molecular energetics is illusory when the methods are compared on the same basis.     

Differentiation of the isomeric 1,2-cyclopentanediols by ion-molecule reactions in a triple-quadrupole mass spectrometer

Collisionally activated decompositions and ion-molecule reactions in a triple-quadrupole mass spectrometer are used to distinguish between cis- and trans-1,2-cyclopentanediol isomers. For ion kinetic energies varying from 5 eV to 15 eV (laboratory frame of reference), qualitative differences in the daughter ion spectra of [MH]⁺ are seen when N₂ is employed as an inert collision gas. The cis ?1,2-cyclopentanediol isomer favors H₂O elimination to give predominantly [MH- H₂O]⁺. In the trans isomer, where H₂O elimination is less likely to occur, the rearrangement ion [HOCH₂CHOH]⁺ exists in significantly greater abundance. Ion-molecule reactions with NH₃ under single-collision conditions and low ion kinetic energies can provide thermochemical as well as stereochemical information. For trans ?1,2-cyclopentanediol, the formation of [NH₄]⁺ by proton transfer is an exothermic reaction with the maximum product ion intensity at ion kinetic energies approaching 0 eV. The ammonium adduct ion [M + NH₄]⁺ is of greater intensity for the trans isomer. In the proton transfer reaction with the cis isomer, the formation of [NH₄]⁺ is an endothermic process with a definite translational energy onset. From this measured threshold ion kinetic energy, the proton affinity of cis ?1,2-cyclopentanedioi was estimated to be 886 ± 10 kJ mol^?1.     

A DFT study of proton transfers for the reaction of phenol and hydroxyl radical leading to dihydroxybenzene and H2O in the water cluster

Reactions of phenol and hydroxyl radical were studied under the aqueous environment to investigate the antioxidant characters of phenolic compounds. M06‐2X/6‐311 + G(d,p) calculations were carried out, where proton transfers via water molecules were examined carefully. Stepwise paths from phenol + OH^• + (H₂O)_n (n = 3, 7, and 12) to the phenoxyl radical (Ph O^•) via dihydroxycyclohexadienyl radicals (ipso, ortho, meta, and para OH‐adducts) were obtained. In those paths, the water dimer was computed to participate in the bond interchange along hydrogen bonds. The concerted path corresponding to the hydrogen atom transfer (HAT, apparently Ph OH + OH^• → Ph O^• + H₂O) was found. In the path, the hydroxyl radical located on the ipso carbon undergoes the charge transfer to prompt the proton (not hydrogen) transfer. While the present new mechanism is similar to the sequential proton loss electron transfer (SPLET) one, the former is of the concerted character. Tautomerization reactions of ortho or para (OH)C₆H₅=O + (H₂O)_n → C₆H₄(OH)₂(H₂O)_n were traced with n = 2, 3, 4, and 14. The n = 3 (and n = 14) model of ortho and para was calculated to be most likely by the strain‐less hydrogen‐bond circuit.     

Chiral Transformation in Protonated and Deprotonated Adipic Acids through Multistep Internal Proton Transfer

Protonated and deprotonated adipic acids (PAA: HOOC? (CH₂)₄? COOH₂⁺ and DAA: HOOC? (CH₂)₄? COO^?) have a charged hydrogen bond under the influence of steric constraint due to the molecular skeleton of a circular ring. Despite the similarity between PAA and DAA, it is surprising that the lowest energy structure of PAA is predicted to have (H₂O???H???OH₂)⁺ Zundel‐like symmetric hydrogen bonding, whereas that of DAA has H₃O⁺ Eigen‐like asymmetric hydrogen bonding. The energy profiles show that direct proton transfer between mirror image structures is unfavorable. Instead, the chiral transformation is possible by subsequent backbone twistings through stepwise proton transfer along multistep intermediate structures, which are Zundel‐like ions for PAA and Eigen‐like ions for DAA. This type of chiral transformation by multistep intramolecular proton transfers is unprecedented. Several prominent OH???O short hydrogen‐bond stretching peaks are predicted in the range of 1000–1700 cm^?1 in the Car–Parrinello molecular dynamics (CPMD) simulations, which show distinctive signatures different from ordinary hydrogen‐bond peaks. The O? H? O stretching peaks in the range of 1800–2700 cm^?1 become insignificant above around 150 K and are almost washed out at about 300 K.     

Solvent‐Vapor‐Induced Reversible Single‐Crystal‐to‐Single‐Crystal Transformation of a Triphosphaazatriangulene‐Based Metal–Organic Framework

A triphosphaazatriangulene (H₃L) was synthesized through an intramolecular triple phospha‐Friedel–Crafts reaction. The H₃L triangulene contains three phosphinate groups and an extended π‐conjugated framework, which enables the stimuli‐responsive reversible transformation of [Cu(HL)(DMSO)?(MeOH)]_n, a 3D‐MOF that exhibits reversible sorption characteristics, into (H₃L?0.5 [Cu₂(OH)₄?6 H₂O] ?4 H₂O), a 1D‐columnar assembled proton‐conducting material. The hydrophilic nature of the latter resulted in a proton conductivity of 5.5×10^?3 S cm^?1 at 95 % relative humidity and 60 °C.     

MNDO study of fragmentations in mass spectrometry. Part I. The geometry and electron structure of [C3H6O] + ˙ systems and [C2H3O]+ ions

MNDO calculations of [C₃H₆O]^{+ ˙} predict the parallel existence of both structures of radical cations of acetone (1) and propen-2-ol (2) in electron ionization spectra. The calculated heats of formation of 1^{+ ˙} (ΔH_f^MNDO = 783.2 kj mol^?1) and of 2^{+ ˙} (ΔH_f^MNDO = 649.8 kJ mol^?1) are in very good agreement with the experimental results. A comparison with the results of ab initio calculations (3–21 G and 6–31 G) and experimental data for the individual structures of the main fragment [C₂H₃O]⁺ demonstrates a sufficient accuracy of MNDO results, suggesting the possibility of applying the method also in other cationic systems, especially in larger ones.     

Ab initio studies of H2PXYH molecules (X,Y = O,S)

Ab initio molecular orbital theory is applied to the study of P? O and P? S bonding in the hypervalent phosphinic (H₂POOH), phosphinothioic (H₂POSH), and phosphinodithioic (H₂PSSH) acid molecules. Intramolecular proton exchange reactions are followed using the intrinsic reaction coordinate and Self-Consistent-Field energy localized orbitals. The P? O and PS bonds are characterized via force constants, phosphorus d orbital populations, and localized orbitals and are best described as either normal single bonds or dative bonds augmented by π back donation from the oxygen or sulfur lone pairs. The anions of these acids are also investigated, and they are found to contain only dative bonds to sulfur and oxygen.     

Synthesis,characterization and properties of polyaniline doped with transition metal substituted silicotungstate

Polyaniline hybrid material doped with transition metal mono-substituted silicotungstate β₂-K₆[SiW₁₁M(H₂O)O₃₉]?·?xH₂O (M?=?Mn²⁺, Co²⁺, Cu²⁺, Fe²⁺) were prepared for the first time. Their scanning electron microscopy (SEM), infrared (IR), UV–Vis, and X-ray diffraction (XRD) patterns confirm the existence of Keggin anions and form the space reticular structure. The material exhibits excellent proton conduction, its proton conductivity is 9?×?10^?2?s?cm^?1 at room temperature (20°C).     

The Intermolecular S?H⋅⋅⋅Y (Y=S,O) Hydrogen Bond in the H2S Dimer and the H2S–MeOH Complex

The nature of the S? H???S hydrogen‐bonding interaction in the H₂S dimer and its structure has been the focus of several theoretical studies. This is partly due to its structural similarity and close relationship with the well‐studied water dimer and partly because it represents the simplest prototypical example of hydrogen bonding involving a sulfur atom. Although there is some IR data on the H₂S dimer and higher homomers from cold matrix experiments, there are no IR spectroscopic reports on S? H???S hydrogen bonding in the gas phase to‐date. We present experimental evidence using VUV ionization‐detected IR‐predissociation spectroscopy (VUV‐ID‐IRPDS) for this weak hydrogen‐bonding interaction in the H₂S dimer. The proton‐donating S? H bond is found to be red‐shifted by 31 cm^?1. We were also able to observe and assign the symmetric (ν₁) stretch of the acceptor and an unresolved feature owing to the free S? H of the donor and the antisymmetric (ν₃) SH stretch of the acceptor. In addition we show that the heteromolecular H₂S–MeOH complex, for which both S? H???O and O? H???S interactions are possible, is S‐H???O bound.     

Theoretical studies on the structure and protonation of Cu(II) complexes of a series of tripodal aliphatic tetraamines: Good correlations with the experimental data

DFT(B3LYP) studies on first protonation step of a series of Cu(II) complexes of some tripodal tetraamines with general formula N[(CH₂)_nNH₂][(CH₂)_mNH₂][(CH₂)_pNH₂] (n = m = p = 2, tren; n = 3, m = p = 2, pee; n = m = 3, p = 2, ppe; n = m = 3, tpt; n = 2, m = 3, p = 4, epb; and n = m = 3, p = 4; ppb) are reported. First, the gas‐phase proton macroaffinity of all latter complexes was calculated with considering following simple reaction: [Cu(L)]²⁺(g) + H⁺(g) → [Cu(HL)]³⁺(g). The results showed that there is a good correlation between the calculated proton macroaffinities of all complexes with their stability constants in solution. Then, we tried to determine the possible reliable structures for microspecies involved in protonation process of above complexes. The results showed that, similar to the solid state, the [Cu(L)(H₂O)]²⁺ and [Cu(HL)(H₂O)₂]³⁺ are most stable species for latter complexes and their protonated form, respectively, at gas phase. We found that there are acceptable correlations between the formation constants of above complexes with both the ? and ? of following reaction: [Cu(L)(H₂O)]²⁺(g) + H⁺(g) + H₂O(g) → [Cu(HL)(H₂O)₂]³⁺(g). The ? of the latter reaction can be defined as a theoretically solvent–proton macroaffinity of reactant complexes because they have gained one proton and one molecule of the solvent. The unknown formation constant of [Cu(epb)]²⁺ complex was also predicted from the observed correlations. In addition, the first proton affinity of all complexes was studied in solution using DPCM and CPCM methods. It was shown that there is an acceptable correlation between the solvent–proton affinities of [Cu(L)(H₂O)]²⁺ complexes with formation constants of [Cu(HL)(H₂O)₂]³⁺ complexes in solution. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Mechanism of formic acid decomposition on P?Mo heteropolyacid

Hydrated (undecomposed) form of heteropolyacid H₃PMo₁₂O₄₀/SiO₂ exhibits a higher activity in the formic acid decomposition than the corresponding dehydrated sample. The formic acid decomposition takes place on strong Br?nsted acid sites of the heteropolyacid.Ab initio SCF MO LCAO method was used for the calculation of the electronic state of two surface complexes of HCOOH molecule (S1 and S2) coordinated to a proton H⁺. The S1 complex is formed by proton addition to the carbonyl oxygen, whereas the S2 complex is formed proton addition to the oxygen atom of the C−O−H fragment of HCOOH. The selective weakening of the C−O bond and localization of the positive charge on the (O=C−H) fragment in the protonated complex S2 are favorable for the decomposition of formic acid to CO and H₂O.     

Kinetics and mechanism of the oxidation of primary alcohols by sodium N-chloroethylcarbamate

The oxidation of primary alcohols by sodium N-chloroethylcarbamate in acid solution, results in the formation of corresponding aldehydes. The reaction is first order with respect to the oxidant and alcohol. The rate increases with an increase in acidity. The oxidation of α,α-dideuterioethanol exhibited a primary kinetic isotope, k_H/k_D = 2.11 at 298 K. The value of solvent isotope effect k(H₂O)/k(D₂O) = 2.23 at 298 K. Addition of ethyl carbamate does not affect the rate. (EtOC(OH)NHCl)⁺ has been postulated as the reactive species. Plots of (log k₂ + Ho) against (Ho + log[H⁺]) are linear with the slope, ?, having values from 1.78–1.87. This suggested a proton abstraction by water in the rate-determining step. The rates of oxidation of alcohols bearing both electron-withdrawing and electron-donating groups are more than that of methanol. A concerted mechanism involving transfer of a hydride ion from the C? H bond of the alcohol tothe oxidant and removal of a proton from the O? H group by a water molecule has been proposed.     

正硅酸乙酯水解过程的半经验量子化学研究

通过半经验量子化学方法研究了正硅酸乙酯的最优化分子几何结构并推断了催化水解机理。通过用MNDO方法求得正硅酸乙酯在不同条件下水解反应过程的位能曲线,研究了不同催化剂对正硅酸乙酯水解反应过程的影响。计算结果表明,碱催化过程是一个放热过程,硅原子可从原先的4配位的正四面体结构向6配位的八面体结构转变。而在酸性条件下,水合质子作为亲电试剂,可以使正硅酸乙酯的烷氧基质子化,从而增加了正硅酸乙酯的亲电能力。质子化后的正硅酸乙酯容易被亲核试剂所进攻,进攻过程是一个S_N2亲核取代反应过程。计算结果表明,在有氟离子参与的反应过程中,氟离子对正硅酸乙酯亲核进攻所形成的6配位结构易与亲核试剂水分子发生亲核反应。这些结论对实验研究将起到很重要的指导意义。     

Further examples of skeletal rearrangements of the Wagner-Meerwein type in chemical ionization mass spectrometry: The case of [C6H9]+ ions

The [C₆H₉]⁺ ions produced either via unimolecular H₂O loss from 13 [C₆H₁₁O]⁺ precursors or direct protonation of 1,3- and 1,4-cyclohexadiene have identical collisional activation mass spectra. The kinetic energy release data for the process [C₆H₁₁O]⁺→[C₆H₉]⁺+H₂O are also very similar (on average T_0.5=24 meV) irrespective of the constitution of the precursor. From the proton affinities of 1,3-cyclohexadiene (PA=837.2 kJ mol^?1) using ion cyclotron resonance mass spectrometry the heat of formation of the [C₆H₉]⁺ ion is determined to 804.6 kJ mol^?1. This value taken together with the results of molecular orbital calculations (MNDO) and the structure indicative losses of CH₃^. and C₂H₄ upon collisional activation suggest that the [C₆H₉]⁺ ion has the structure of the 1-methylcyclopentenylium ion f and not that of the slightly less stable cyclohexenylium ion g. The generator of an easily interconverting system of isomeric [C₆H₉]⁺ ions is unlikely to be due to the high barrier separating the various isomers.     

Molecular orbital treatments of hydrogen bonded systems. 2. Dimers of water and HCN

Calculations were performed to investigate the reliabilities of the CNDO/2, PRDDO, and MNDO approximate molecular orbital methods. Systems selected for study included the linear, cyclic, and bifurcated dimers of water as well as the linear and cyclic dimers of HCN. The PRDDO method was found to provide the most consistently accurate reproduction of ab initio and experimental data. CNDO/2 performed fairly well in a number of cases but yielded extremely poor results for the cyclic dimers of both H₂O and HCN. Hydrogen bond strengths were consistently underestimated by MNDO which also furnished erroneously large intermolecular separations. In addition, MNDO calculations indicate the bifurcated water dimer to be most stable in contrast to other quantum mechanical and experimental information.See Ref. [1] for Paper 1 of this series.     

The 1:1 adduct of 4‐aminobenzoic acid with 4‐aminobenzonitrile

The 1:1 adduct of 4‐amino­benzoic acid (PABA) with 4‐am‐inobenzonitrile (PABN), C₇H₇NO₂·C₇H₆N₂, consists of a primary centrosymmetric cyclic hydrogen‐bonded PABA dimer interaction [O?O 2.640 (3) Å] peripherally linked into chains by weaker hydrogen bonds via a head‐to‐tail PABN interaction [N?N 3.179 (4) and N?O 3.062 (4) Å], and is linked between the chains by amine‐N (PABN) to amine‐N (PABA) interactions [N?N 3.233 (5) Å]. No proton transfer occurs.